rrnni-package {rrnni}R Documentation

rrnni: Calculate a distance and a path in RNNI space

Description

RNNI stands for Ranked Nearest Neighbour Interchange and is an extension of the classical NNI space (space of trees created by the NNI moves) to ranked trees, where internal nodes are ordered according to their heights (usually assumed to be times). Since ranked trees are variants of time trees, they keep the biologically relevant information about the timing of events, such as splits. Note that we assume ultrametric trees, i.e. all leaves have the same time, and unique order of internal nodes, which means that two non-leaf nodes cannot have the same time.

Details

The RNNI distance takes the tree topology into account, as standard NNI does, but also penalizes changes in the order of internal nodes, i.e. changes in the order of times of evolutionary events.

Author(s)

Maintainer: Jiří C. Moravec jiri.c.moravec@gmail.com

Authors:

References

Gavryushkin, A., Whidden, C., Matsen, IV. F. A. (2018). The combinatorics of discrete time-trees: theory and open problems. Journal of Mathematical Biology, 76(5):1101-1121. doi: 10.1007/s00285-017-1167-9

Collienne, L. and Gavryushkin A. (2021). Computing Nearest Neighbour Interchange Distances Between Ranked Phylogenetic Trees. Journal of Mathematical Biology, 82(1-2):8. doi: 10.1007/s00285-021-01567-5

Collienne, L. (2021). Spaces of Phylogenetic Time Trees. University of Otago.

See Also

Useful links:


[Package rrnni version 0.1.1 Index]